Plant genetics and statistics
1.6K views | +0 today
Follow
Plant genetics and statistics
research, news and opinions on plant genetics and statistics with emphasis on forage crop breeding and molecular plant ecology
Your new post is loading...
Your new post is loading...
Scooped by Roland Kölliker
Scoop.it!

Food crop varieties endangered as scientists rush to save them

Food crop varieties endangered as scientists rush to save them | Plant genetics and statistics | Scoop.it
About 15 years ago, Ms Sarah Namubiru’s family used to grow nylon and kyebadula potato varieties in Luweero District
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Scientists Uncover New Antiviral Defense Mechanism In Rice

Scientists Uncover New Antiviral Defense Mechanism In Rice | Plant genetics and statistics | Scoop.it
Chinese researchers have revealed a new antiviral mechanism in rice, a discovery that could boost control against viral epidemics and guarantee food security.
more...
No comment yet.
Rescooped by Roland Kölliker from Microbes, plant immunity, and crop science
Scoop.it!

Profiling the extended phenotype of plant pathogens

Profiling the extended phenotype of plant pathogens | Plant genetics and statistics | Scoop.it
“ One of the most fundamental questions in plant pathology is what determines whether a pathogen grows within a plant? This question is frequently studied in terms of the role of elicitors and pathogenicity factors in the triggering or overcoming of host defences. However, this focus fails to address the basic question of how the environment in host tissues acts to support or restrict pathogen growth. Efforts to understand this aspect of host–pathogen interactions are commonly confounded by several issues, including the complexity of the plant environment, the artificial nature of many experimental infection systems and the fact that the physiological properties of a pathogen growing in association with a plant can be very different from the properties of the pathogen in culture. It is also important to recognize that the phenotype and evolution of pathogen and host are inextricably linked through their interactions, such that the environment experienced by a pathogen within a host, and its phenotype within the host, is a product of both its interaction with its host and its evolutionary history, including its co-evolution with host plants. As the phenotypic properties of a pathogen within a host cannot be defined in isolation from the host, it may be appropriate to think of pathogens as having an ‘extended phenotype’ that is the product of their genotype, host interactions and population structure within the host environment. This article reflects on the challenge of defining and studying this extended phenotype, in relation to the questions posed below, and considers how knowledge of the phenotype of pathogens in the host environment could be used to improve disease control. What determines whether a pathogen grows within a plant? What aspects of pathogen biology should be considered in describing the extended phenotype of a pathogen within a host? How can we study the extended phenotype in ways that provide insights into the phenotypic properties of pathogens during natural infections?”
Via Nicolas Denancé
more...
No comment yet.
Rescooped by Roland Kölliker from Microbes, plant immunity, and crop science
Scoop.it!

Genome editors take on crops

Genome editors take on crops | Plant genetics and statistics | Scoop.it
“ The global population is expected to rise from 7.3 billion to 9.7 billion by 2050 ( 1 ). At the same time, climate change poses increasing risks to crop production through droughts and pests ( 2 ). Improved crops are thus urgently needed to meet growing demand for food and address changing climatic conditions. Genome-editing technologies such as the CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated protein) system ( 3 ) show promise for helping to address these challenges, if the precision of genome editing is improved and the technology is approved and accepted by regulators, producers, and consumers.”
Via Loïc Lepiniec, Nicolas Denancé
more...
No comment yet.
Rescooped by Roland Kölliker from Microbes, plant immunity, and crop science
Scoop.it!

Phytopathol.: Characterization of the Xanthomonas translucens Complex Using Draft Genomes, Comparative Genomics, Phylogenetic Analysis, and Diagnostic LAMP Assays

Prevalence of Xanthomonas translucens, which causes cereal leaf streak (CLS) in cereal crops and bacterial wilt in forage and turfgrass species, has increased in many regions in recent years. Because the pathogen is seedborne in economically important cereals, it is a concern for international and interstate germplasm exchange and, thus, reliable and robust protocols for its detection in seed are needed. However, historical confusion surrounding the taxonomy within the species has complicated the development of accurate and reliable diagnostic tools for X. translucens. Therefore, we sequenced genomes of 15 X. translucens strains representing six different pathovars and compared them with additional publicly available X. translucens genome sequences to obtain a genome-based phylogeny for robust classification of this species. Our results reveal three main clusters: one consisting of pv. cerealis, one consisting of pvs. undulosa and translucens, and a third consisting of pvs. arrhenatheri, graminis, phlei, and poae. Based on genomic differences, diagnostic loop-mediated isothermal amplification (LAMP) primers were developed that clearly distinguish strains that cause disease on cereals, such as pvs. undulosa, translucens, hordei, and secalis, from strains that cause disease on noncereal hosts, such as pvs. arrhenatheri, cerealis, graminis, phlei, and poae. Additional LAMP assays were developed that selectively amplify strains belonging to pvs. cerealis and poae, distinguishing them from other pathovars. These primers will be instrumental in diagnostics when implementing quarantine regulations to limit further geographic spread of X. translucens pathovars.

Via Nicolas Denancé
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

12 ways that research is changing the food of the future

12 ways that research is changing the food of the future | Plant genetics and statistics | Scoop.it
Across the world, tens of thousands of scientists are looking at ways to improve our food. The stuff we put on our plates already looks a lot different from the wild varieties domesticated by our ancestors around 10,000 years ago.
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Freeing Crop Genetics through the Open Source Seed Initiative

Freeing Crop Genetics through the Open Source Seed Initiative | Plant genetics and statistics | Scoop.it
This Community Page article highlights the Open Source Seed Initiative, which serves as an alternative to restrictive intellectual property rights and is working to develop an open-source release mechanism for crop plant diversity, analogous to...
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

CRISPR creates a way out of regulation for GMO food

CRISPR creates a way out of regulation for GMO food | Plant genetics and statistics | Scoop.it
Genetically modified crops are in the midst of a metamorphosis thanks to new gene-editing technology. The latest example is a white button mushroom..
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Statisticians issue warning over misuse of P values

Statisticians issue warning over misuse of P values | Plant genetics and statistics | Scoop.it
Policy statement aims to halt missteps in the quest for certainty.
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Plant Breeding Matters | Improving our everyday lives

How innovation in plant breeding touches everyone's lives for the better - from the improved availability of healthier, tastier food to our enjoyment o
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Error Control in Exploratory ANOVA’s: The How and the Why

Error Control in Exploratory ANOVA’s: The How and the Why | Plant genetics and statistics | Scoop.it

In a 2X2X2 design, there are three main effects, three two-way interactions, and one three-way interaction to test. That’s 7 statistical tests.The probability

more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

New Study: Research Says Plants Do Not Want to be Eaten

New Study: Research Says Plants Do Not Want to be Eaten | Plant genetics and statistics | Scoop.it

We found that feeding vibrations signal changes in the plant cells' metabolism, creating more defensive chemicals that can repel attacks from caterpillars.- Heidi Appel

more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

My note on multiple testing

It's not a shame to put a note on something (probably) everyone knows and you thought you know but actually you are not 100% sure.

more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Add ‘light bulbs growing on trees’ to ‘flying cars’ on your list of things Science didn’t bring you for Christmas

Add ‘light bulbs growing on trees’ to ‘flying cars’ on your list of things Science didn’t bring you for Christmas | Plant genetics and statistics | Scoop.it
There once was a kickstarter that raised half a million dollars with the idea of genetically modifying trees to glow in the dark, thereby replacing the need for street lights. It failed. I’m …
Roland Kölliker's insight:
It's not always that easy...
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Researchers Sequence Barley Genome | Genetics | Sci-News.com

Researchers Sequence Barley Genome | Genetics | Sci-News.com | Plant genetics and statistics | Scoop.it
The International Barley Genome Sequencing Consortium, which is led by Dr. Nils Stein of the Leibniz Institute of Plant Genetics and Crop Plant Research, Germany, has mapped the entire genome of barley (Hordeum vulgare), the world’s fourth most important cereal crop after wheat, rice and maize. The research appears in the journal Nature.
more...
No comment yet.
Rescooped by Roland Kölliker from Microbes, plant immunity, and crop science
Scoop.it!

Plant physiol.: Hierarchically aligning 10 legume genomes establishes a family-level genomics platform (2017)

Plant physiol.: Hierarchically aligning 10 legume genomes establishes a family-level genomics platform (2017) | Plant genetics and statistics | Scoop.it
Mainly due to their economic importance, genomes of 10 legumes, including soybean, wild peanuts, barrel medic, etc, have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by wide-spread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported a likely autopolypoidy nature of its tetraploid ancestor. Moreover, though mostly gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes, and by performing Ks correction, re-dated major evolutionary events during their expansion. The present effort laid a solid foundation further genomics exploration in the legume research community and beyond. We described only a tiny fraction of legume comparative genomics analysis that we performed, and more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org).

Via Nicolas Denancé
more...
No comment yet.
Rescooped by Roland Kölliker from Plants and Microbes
Scoop.it!

PNAS: Live imaging of root–bacteria interactions in a microfluidics setup (2017)

PNAS: Live imaging of root–bacteria interactions in a microfluidics setup (2017) | Plant genetics and statistics | Scoop.it

Plant roots play a dominant role in shaping the rhizosphere, the environment in which interaction with diverse microorganisms occurs. Tracking the dynamics of root–microbe interactions at high spatial resolution is currently limited because of methodological intricacy. Here, we describe a microfluidics-based approach enabling direct imaging of root–bacteria interactions in real time. The microfluidic device, which we termed tracking root interactions system (TRIS), consists of nine independent chambers that can be monitored in parallel. The principal assay reported here monitors behavior of fluorescently labeled Bacillus subtilis as it colonizes the root of Arabidopsis thaliana within the TRIS device. Our results show a distinct chemotactic behavior of B. subtilis toward a particular root segment, which we identify as the root elongation zone, followed by rapid colonization of that same segment over the first 6 h of root–bacteria interaction. Using dual inoculation experiments, we further show active exclusion of Escherichia coli cells from the root surface after B. subtilis colonization, suggesting a possible protection mechanism against root pathogens. Furthermore, we assembled a double-channel TRIS device that allows simultaneous tracking of two root systems in one chamber and performed real-time monitoring of bacterial preference between WT and mutant root genotypes. Thus, the TRIS microfluidics device provides unique insights into the microscale microbial ecology of the complex root microenvironment and is, therefore, likely to enhance the current rate of discoveries in this momentous field of research.


Via IPM Lab, Kamoun Lab @ TSL
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

GM crop planting declines for the first time

GM crop planting declines for the first time | Plant genetics and statistics | Scoop.it
Total area sown with genetically modified plants fell 1% in 2015.
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Impact of plant domestication on rhizosphere microbiome assembly and functions | SpringerLink

Impact of plant domestication on rhizosphere microbiome assembly and functions | SpringerLink | Plant genetics and statistics | Scoop.it
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses.
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Vital Plant Communication with Bacteria and Fungus

Vital Plant Communication with Bacteria and Fungus | Plant genetics and statistics | Scoop.it
Building complex structures for survival to obtain the all-important nitrogen fixation, depends upon vital plant communication with bacteria and fungus
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

20 Cool Tools for Creating Infographics

20 Cool Tools for Creating Infographics | Plant genetics and statistics | Scoop.it
Imagine if you could create an infographic in under 10 minutes without being a designer? Discover 20 tools that will help you when creating infographics.
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

11 Important Model Evaluation Techniques Everyone Should Know

11 Important Model Evaluation Techniques Everyone Should Know | Plant genetics and statistics | Scoop.it
Model evaluation metrics are used to assess goodness of fit between model and data, to compare different models, in the context of model selection, and to pred…
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

The Top 10 Retractions of 2015 | The Scientist Magazine®

The Top 10 Retractions of 2015 | The Scientist Magazine® | Plant genetics and statistics | Scoop.it
A look at this year’s most memorable retractions
more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

Breeding higher yielding crops by increasing sugar import into seeds

Breeding higher yielding crops by increasing sugar import into seeds | Plant genetics and statistics | Scoop.it

Once a mother plant releases its embryos to the outside world, they have to survive on their own without family protection.

more...
No comment yet.
Scooped by Roland Kölliker
Scoop.it!

What have plants ever done for us?

What have plants ever done for us? | Plant genetics and statistics | Scoop.it

They provide the food we eat, the medicines we take, the fuel we use – and, of course, the oxygen we breathe. Plants have been indispensable to human beings for millennia, having a profound and often unexpected impact on our everyday lives.

more...
No comment yet.